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BCHM Mod 3 > Section 7 > Flashcards

Section 7 Flashcards

1
Q

What are the key requirements for chromosome packaging?

A

Chromosome packaging must be highly organized, allow access to factors that regulate DNA replication, and allow access to factors that regulate transcription.

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2
Q

What are the basic building blocks of DNA?

A

Nucleotides, which contain a nitrogenous base, a pentose sugar, and a phosphate group. The four nucleotides are A, T, C, and G.

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3
Q

What is the structure formed when two antiparallel strands of DNA wind around each other via base pairing?

A

DNA Double Helix.

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4
Q

What are the basic proteins that associate tightly with DNA in eukaryotic cells and help condense DNA?

A

Histones.

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5
Q

What is the structural unit for packaging chromatin in eukaryotes, consisting of a DNA strand wound around a histone core?

A

Nucleosome.

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6
Q

What is the term for a filamentous complex of DNA, histones, and other proteins, constituting the eukaryotic chromosome?

A

Chromatin.

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7
Q

What is a single large DNA molecule and its associated proteins?

A

Mitotic Chromosome.

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8
Q

What are the major protein components of chromatin?

A

Histones.

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9
Q

How do histones assemble, and what is their basic structure?

A

Histones assemble into octamers, each consisting of two copies of four different histone subunits.

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10
Q

In the first level of chromosome packaging, how is DNA arranged around histone octamers, and what is this structure called?

A

DNA is wrapped twice around histone octamers, forming a structure known as a nucleosome.

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11
Q

Why can histone proteins interact with the DNA backbone, and how does this interaction occur?

A

The positive charge of histone proteins allows them to interact with the negatively charged DNA backbone through electrostatic interactions.

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12
Q

What is Giemsa stain used for in cytogenetics?

A

Giemsa stain is used to create banding patterns on chromosomes.

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13
Q

What is heterochromatin, and how is it represented in banding patterns?

A

Heterochromatin is a portion of the genome that is generally not transcriptionally active. It appears as dark bands on the chromosome banding patterns and consists of condensed DNA.

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14
Q

What is euchromatin, and how is it represented in banding patterns?

A

Euchromatin is the transcriptionally active portion of the human genome. It appears as light regions in chromosome banding patterns, and its DNA is less compact compared to heterochromatin.

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15
Q

Increase in darkness = ______ in condensation = _______ in transcriptional activity

A

Increase in darkness =
INCREASE in condensation (tight packing) =
DECREASE in transcriptional activity

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16
Q

What is each of the following in relation to one another;
Chromatin, nucleosomes, histones

A

Chromatin:
- highest level of DNA structure
- DNA & protein making up chromosomes

Nucleosomes:
- unit of chromatin
- made up of DNA wrapped around a set of proteins called the histone core

Histones:
- basic proteins
- assemble into octameric complexes
- highly positively charged (makes sense for counteracting the negative charge of DNA backbone)

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17
Q

What is the purpose of chemical crosslinking in Kornberg’s experiments?

A

Chemical crosslinking is used to identify proteins that are in close proximity, revealing their structural relationships

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18
Q

Which histone subunits form a heterotetramer in the histone octamer?

A

H3 and H4 form a heterotetramer within the histone octamer.

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19
Q

According to Kornberg’s findings, how is the histone octamer composed?

A

The histone octamer consists of two copies of each core histone: H2A, H2B, H3, and H4. H2A and H2B form a tetramer that assembles into the octamer.

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20
Q

What is the function of the linker histone (H1) in chromatin structure?

A

The linker histone (H1) binds to the nucleosome and protects the linker DNA between nucleosomes from degradation.

It also aids with higher order compaction.

It is NOT part of the histone octomer

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21
Q

Does the histone octamer require something to assemble, or is it spontaneous?

A

It requires the presence of DNA and chaperone proteins to assemble.

It will not assemble spontaneously. It needs the neutralization of charge in order to assemble

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22
Q

True or false:

H1 is a part of the histone octomer

A

False

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23
Q

The histone octamer comprises:

One copy of H1, two H2A-H2B dimers and one H3-H4 tetramer

Two H2A-H2B dimers and two H3-H4 dimers

Two H2A-H2B dimers and one H3-H4 tetramer

Two H3-H4 dimers and one H2A-H2B tetramer

One copy of H1, two H2A-H2B dimers and two H3-H4 dimers

A

Two H2A-H2B dimers and one H3-H4 tetramer

H1 is not a part of the octamer

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24
Q

As a DNA packaging protein for the entire genome, it is important for histones to bind DNA via sequence-specific interactions with the major groove.

True
False

A

False

you want histone to be generic so it can interact with more stuff

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25
Q

Describe the structure of the histone-fold motif.

A

The histone-fold motif consists of a globular domain composed of three α-helices linked by two short loops.

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26
Q

How does the 3D structure of the histone-fold motif enable histone proteins to interact?

A

The 3D structure of the histone-fold motif allows histone proteins to form dimers, either H3-H4 or H2A-H2B, facilitating the tight wrapping of DNA to create a nucleosome.

27
Q

How do the histone proteins interact with the DNA molecule?

A

The histone subunits interact with the DNA molecule primarily through electrostatic interactions between the negatively charged sugar-phosphate backbone of DNA and the positively charged Lys and Arg residues of the histone fold.

28
Q

How is the 3D structure of a histone-fold dimer arranged in the nucleosome?

A

The 3D structure of each histone-fold dimer forms a V-shaped structure with three DNA-binding sites.

29
Q

How does the nucleosome interact with DNA, and where on the DNA does it bind?

A

The nucleosome interacts with DNA via the minor groove, and it binds to the DNA at all three DNA-binding sites.

30
Q

For histone-DNA interactions, the regions of DNA where the minor groove comes in contact with the histone octamer experience significant compaction. This compaction would be facilitated by an abundance of:

A-T pairings
G-C pairings
The type of pairing doesn’t matter

A

A-T pairings

A-T pairs are more compressible (only two hydrogen bonds)
vs GC have 3, they are stronger but less compressible

31
Q

How does a local abundance of A=T base pairs in the minor groove of DNA affect nucleosome binding?

A

A local abundance of A=T base pairs in the minor groove of DNA facilitates the compression of the minor groove, which is needed for tight wrapping of DNA around the histone octamer.

32
Q

Why do histone octamers assemble particularly well with sequences that have two or more A=T base pairs staggered at 10 bp intervals?

A

Histone octamers assemble well with sequences where two or more A=T base pairs are staggered at 10 bp intervals because DNA is naturally bent at these sequences, facilitating nucleosome formation.

33
Q

How do tracts of G≡C base pairs affect nucleosome binding?

A

Tracts of G≡C base pairs have the opposite effect to A=T base pairs; they prevent compression of the minor groove, making them preferred at positions not facing nucleosomes.

34
Q

Each nucleosome contains:
A) Four proteins: H2A, H2B, H3, and H4.
B) A histone octamer composed of two copies of each of the following proteins: H1, H2A, H2B,
H3, and H4.
C) Four proteins: SMC1, SMC2, SMC3, and SMC4.
D) A mixture of histone and SMC proteins.

A

C) A histone octamer composed of two copies of each of the following proteins: H1, H2A, H2B,
H3, and H4.

35
Q

When the H1 is bound to the histone octamer and DNA,this structure is known as the __________.

A

chromatosome

36
Q

What is the structural unit formed when DNA wraps around an octamer of histone proteins?

A

The structural unit formed when DNA wraps around an octamer of histone proteins is called a nucleosome.

37
Q

What is the fifth histone protein that binds to the nucleosome in the DNA linker region?

A

The fifth histone protein that binds to the nucleosome in the DNA linker region is H1.

38
Q

How many DNA-binding sites does the histone H1 have?

A

The histone H1 has two DNA-binding sites.

39
Q

What is the function of H1 when it binds to DNA in the chromatosome?

A

When H1 binds to DNA in the chromatosome, it provides protection to the linker DNA between two adjacent nucleosomes and further compacts the structure, about 6-7 times more than the nucleosome alone.

40
Q

How many copies of histone H1 are present per histone octamer?

A

Only one copy of histone H1 is present per histone octamer.

41
Q

How is the binding of the histone H1 to the DNA different from the core histones?

A

The histone H1 binds to one strand of the linker DNA as it comes off the nucleosome and binds a second
site in the central region of the DNA helix wrapped around the octamer.

The core histones interact with the
wrapped DNA in the minor groove.

42
Q

Which of the following is NOT a function of histone H1?

  • Stabilizing nucleosomes
  • Promoting higher order chromosome structure
  • Enhancing the repression of transcription by nucleosomes
  • Binding to regions undergoing active RNA synthesis
  • All of these options are functions on H1
A
  • Binding to regions undergoing active RNA synthesis
43
Q

If DNA is packed into units of 200 base pairs, then why are there bands representing lengths
longer than this visible when the digested DNA is run on an agarose gel?

A

The nuclease does not cut the DNA at every single possible spot (although, theoretically it could if the reaction was allowed to go to completion).

Therefore, the bands appear as 200 bp or multiples of 200 bp,
depending on the number of nucleosomes in between each cut.

44
Q

Why must there be a way for the chromatin structure within the promoter region to become accessible?

A

Molecular interactions holding nucleosome arrays together in the 30 nm filament are relatively weak, allowing regions within nucleosome arrays to be dynamic. Hydrogen bonds between histones and DNA can break and re-form easily, enabling access to chromatin for DNA replication and transcription.

45
Q

Chromatin is composed of:

a) DNA
b) Protein
c) DNA and RNA
d) DNA and Protein
e) RNA and protein

A

d) DNA and Protein

46
Q

Why must DNA compaction be dynamic?

A

DNA compaction must be dynamic to allow rapid changes in the degree of condensation as needed during different stages of the cell cycle.

47
Q

What does it mean for DNA compaction to be modifiable?

A

DNA compaction must be globally and locally modifiable, meaning it can be adjusted for processes like mitosis or replication and allow access to specific genes for transcriptional regulation.

48
Q

Why must the compaction system be responsive?

A

The compaction system must be responsive to modification enzymes that can alter the state of DNA condensation, recognizing specific regions for transcription or replication.

49
Q

Why can histones bind to DNA?

A

Because they have lots of positive lysine and arginine residues that help them interact with the negative phosphate-sugar backbone of DNA

50
Q

What is the primary characteristic of the N-terminal histone tails?

A

The N-terminal histone tails are flexible and mostly disordered.

51
Q

How do the histone tails exit the DNA superhelix?

A

The histone tails exit the DNA superhelix through channels formed by the alignment of minor grooves of adjacent DNA helices every 20 base pairs.

52
Q

What role do histone tails play in DNA binding?

A

The histone tails do not contribute much strength to DNA binding, but they organize nucleosomes into a higher-order chromatin structure and form intermolecular contacts (interactions) with adjacent nucleosome particles.

53
Q

How do modifications to histone tails impact nucleosome interactions and chromatin compaction?

A

Modifications to histone tails can decrease interactions between nucleosomes, leading to an increase in DNA access and, consequently, an increase in transcription.

54
Q

What is the role of histone tails in nucleosome-nucleosome interactions and chromatin condensation?

A

Histone tails, particularly those of core histones H4, H3, H2A, and H2B, are essential for nucleosome-nucleosome contacts, regulating chromatin condensation and DNA accessibility. While histone H1 promotes condensation, the N-terminal tails of core histones play a crucial role in filament formation.

55
Q

________________:
A polynucleotide with a specific sequence of deoxyribonucleotide units covalently joined through 3’,5’-phophodiester bonds; serves as the carrier of genetic information

A

Double helix

56
Q

______________________:
The family of basic proteins that associate tightly with DNA in the
chromosomes of all eukaryotic cells and help condense DNA

A

Histone

57
Q

______________:
A thread-like structure, consisting of DNA and histones

A

Chromatin

58
Q

_________________:
The basic structural unit of chromosomes.

A

Nucleosome

59
Q

_____________:
A condensed version of the nucleosome chain that forms upon binding of the histone H1

A

30 nm filament

60
Q

___________________;
A single large DNA molecule containing a discrete part of the genome of an organism

A

Mitotic chromosome

61
Q

What is the ratio of H1:H2A:H2B:H3:H4?

A

There is 1 linker per histone octamer.

Therefore the ratio is 1:2:2:2:2

62
Q

The addition of H1 protein to a section of octamer-bound DNA will:

Enhance transcription
Repress transcription
Have no effect

A

Repress transcription

enhanced compaction means less availability therefore less transcription

63
Q
A

BCHM Mod 3 (9 decks)

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